Clean data for Abundance - size spectra and beavers

Load packages

library(tidyverse)
library(here)
library(knitr)
library(ggdist)
library(readxl)

Flying arthropods

We are going to load the raw data collected by Ph.D. student Valentin Moser and research assistants during June 2021 in eight different beaver dammed streams (Figure 1). They have sampled in two locations: the main pond created by the beaver (i.e. pool factor level within the column location)) and 500 meters upstream of that pond (i.e. control factor level within the column location).

Figure 1: From Moser et al. 2025. Habitat heterogeneity and food availability in beaver-engineered streams foster bat richness, activity and feeding. Journal of Animal Ecology

In the folder data/raw you will find: data_arthropods_flying.xlsx

Flying arthropods were collected by traps like this one:

Figure 2: Example of the trap used to collect flying arthropods. Dr. Cornelia Twining (Eawag) deploys the arthropods trap over the stream water surface. Click on the photo for the credits.

Load raw data

d <- readxl::read_xlsx(path = here("data", "raw","data_arthropods_flying.xlsx"), sheet = 1) |> 
select(-c(sort, remarks))|> # remove unnecesary column
 filter( !is.na(size) ) # remvoe NAs observations
head(d)

# A tibble: 6 × 14
  site  location date  class     order      suborder   family subfamily juvenile
  <chr> <chr>    <chr> <chr>     <chr>      <chr>      <chr>  <lgl>        <dbl>
1 Chrie Control  June  Arachnida Araneae    <NA>       <NA>   NA               0
2 Chrie Control  June  Arachnida Araneae    <NA>       <NA>   NA               0
3 Chrie Control  June  Arachnida Araneae    <NA>       <NA>   NA               0
4 Chrie Control  June  Arachnida Araneae    <NA>       <NA>   NA               0
5 Chrie Control  June  Insecta   Coleoptera Adephaga   Dytis… NA               0
6 Chrie Control  June  Insecta   Coleoptera Phytophaga Curcu… NA               0
# ℹ 5 more variables: terrestrial <dbl>, juv.aquatic <dbl>, unusable <dbl>,
#   size <dbl>, Laufnummer <dbl>

Metadata:

data_dict <- data.frame(
  Column_name = c(
    "site", "location", "date", "class", "order", "suborder", "family",
    "subfamily", "juvenile", "terrestrial", "juv aquatic", "unusable",
    "size", "remarks"
  ),
  Explanation = c(
    "Study system in which the individual was sampled",
    "Site at which individual was sampled (i.e. pool or control)",
    "Collection period during which the individual was sampled (i.e. June or July)",
    "Taxonomic class the sampled individual belongs to",
    "Taxonomic order the sampled individual belongs to",
    "Taxonomic suborder the sampled individual belongs to (where available)",
    "Taxonomic family the sampled individual belongs to (where available)",
    "Taxonomic subfamily the sampled individual belongs to (where available)",
    "Binary value indicating if the sampled individual was a juvenile. 1 = juvenile, 0 = adult",
    "Binary value indicating if the sampled individual was winged. 1 = non-winged, 0 = winged",
    "Binary value indicating if the sampled individual belongs to a taxa with purely aquatic juveniles. 1 = aquatic, 0 = not aquatic",
    "Binary value indicating if the sampled individual came from water (amphipoda, gastropoda)",
    "Length of the sampled individual in mm (rounded to full numbers). Measured from head to end of abdomen, excluding appendages (wings, limbs, antennae, cerci, etc.)",
    "Additional comments or information about a given individual"
  )
)

kable(data_dict, align = c("l","l"), caption = "Metadata for data_arthropods_flying.xlsx")

Metadata for data_arthropods_flying.xlsx

Column_name	Explanation
site	Study system in which the individual was sampled
location	Site at which individual was sampled (i.e. pool or control)
date	Collection period during which the individual was sampled (i.e. June or July)
class	Taxonomic class the sampled individual belongs to
order	Taxonomic order the sampled individual belongs to
suborder	Taxonomic suborder the sampled individual belongs to (where available)
family	Taxonomic family the sampled individual belongs to (where available)
subfamily	Taxonomic subfamily the sampled individual belongs to (where available)
juvenile	Binary value indicating if the sampled individual was a juvenile. 1 = juvenile, 0 = adult
terrestrial	Binary value indicating if the sampled individual was winged. 1 = non-winged, 0 = winged
juv aquatic	Binary value indicating if the sampled individual belongs to a taxa with purely aquatic juveniles. 1 = aquatic, 0 = not aquatic
unusable	Binary value indicating if the sampled individual came from water (amphipoda, gastropoda)
size	Length of the sampled individual in mm (rounded to full numbers). Measured from head to end of abdomen, excluding appendages (wings, limbs, antennae, cerci, etc.)
remarks	Additional comments or information about a given individual

Note

Question:

How many taxa which ones are there?

# Get unique families (excluding NA)
families <- unique(na.omit(d$family))

# Number of unique families
num_families <- length(families)

# Print results
cat("Number of unique families:", num_families, "\n\n")

Number of unique families: 29 

cat("Families:\n")

Families:

print(sort(families))

 [1] "Aphidoidea"    "Cantharidae"   "Carabidae"     "Chrysomelidae"
 [5] "Coccinellidae" "Cucujidae"     "Curculionidae" "Dytiscidae"   
 [9] "Elmidae"       "Erebidae"      "Forficulidae"  "Formicidae"   
[13] "Gerridae"      "Gyrinidae"     "Haliplidae"    "Hydrophilidae"
[17] "Latridiidae"   "Monotomidae"   "Mordellidae"   "Nitidulidae"  
[21] "Notonectidae"  "Panorpidae"    "Phalacridae"   "Psylloidea"   
[25] "Scirtidae"     "Staphylinidae" "Syrphidae"     "Tabanidae"    
[29] "Vespidae"     

Description of the families we have found:

# Families Found Near Streams in Switzerland

families_table <- data.frame(
  Family = c(
    "Aphidoidea", "Cantharidae", "Carabidae", "Chrysomelidae",
    "Coccinellidae", "Cucujidae", "Curculionidae", "Dytiscidae",
    "Elmidae", "Erebidae", "Forficulidae", "Formicidae",
    "Gerridae", "Gyrinidae", "Haliplidae", "Hydrophilidae",
    "Latridiidae", "Monotomidae", "Mordellidae", "Nitidulidae",
    "Notonectidae", "Panorpidae", "Phalacridae", "Psylloidea",
    "Scirtidae", "Staphylinidae", "Syrphidae", "Tabanidae",
    "Vespidae"
  ),
  Description = c(
    "Aphids; plant sap-feeders, often found on riparian vegetation.",
    "Soldier beetles; predatory or nectar-feeding, common in meadows near water.",
    "Ground beetles; many species are predators along stream banks.",
    "Leaf beetles; herbivores on riparian plants.",
    "Lady beetles; mostly aphid predators on vegetation.",
    "Flat bark beetles; live under bark, sometimes in moist riparian wood.",
    "Weevils; herbivores feeding on riparian plants and shrubs.",
    "Predaceous diving beetles; aquatic predators in streams and ponds.",
    "Riffle beetles; aquatic, live attached to stones in running water.",
    "Tiger moths and relatives; larvae feed on diverse plants near water.",
    "Earwigs; omnivores hiding under stones and wood along streams.",
    "Ants; common in soils and vegetation along riparian zones.",
    "Water striders; aquatic predators skating on water surfaces.",
    "Whirligig beetles; fast swimmers on water surfaces in streams.",
    "Crawling water beetles; small herbivorous beetles in shallow water.",
    "Water scavenger beetles; aquatic or semi-aquatic scavengers.",
    "Minute brown scavenger beetles; found in decaying plant matter.",
    "Root-eating beetles; often associated with decaying wood.",
    "Tumbling flower beetles; found on flowers near riparian habitats.",
    "Sap beetles; feed on decaying fruit, fungi, and plant material.",
    "Backswimmers; aquatic predators that swim upside down.",
    "Scorpionflies; scavengers, often in damp shaded stream habitats.",
    "Shining flower beetles; small pollen feeders.",
    "Psyllids; plant sap-feeders, often on riparian trees and shrubs.",
    "Marsh beetles; aquatic or semi-aquatic beetles in wetlands.",
    "Rove beetles; very diverse predators and scavengers in moist habitats.",
    "Hoverflies; larvae are aphid predators, adults visit flowers.",
    "Horse flies; adults feed on blood or nectar, larvae in wet soils.",
    "Wasps; diverse group of predators and parasitoids near water."
  )
)

kable(families_table, caption = "Ecological roles of arthropod families sampled close to streams in Switzerland")

Ecological roles of arthropod families sampled close to streams in Switzerland

Family	Description
Aphidoidea	Aphids; plant sap-feeders, often found on riparian vegetation.
Cantharidae	Soldier beetles; predatory or nectar-feeding, common in meadows near water.
Carabidae	Ground beetles; many species are predators along stream banks.
Chrysomelidae	Leaf beetles; herbivores on riparian plants.
Coccinellidae	Lady beetles; mostly aphid predators on vegetation.
Cucujidae	Flat bark beetles; live under bark, sometimes in moist riparian wood.
Curculionidae	Weevils; herbivores feeding on riparian plants and shrubs.
Dytiscidae	Predaceous diving beetles; aquatic predators in streams and ponds.
Elmidae	Riffle beetles; aquatic, live attached to stones in running water.
Erebidae	Tiger moths and relatives; larvae feed on diverse plants near water.
Forficulidae	Earwigs; omnivores hiding under stones and wood along streams.
Formicidae	Ants; common in soils and vegetation along riparian zones.
Gerridae	Water striders; aquatic predators skating on water surfaces.
Gyrinidae	Whirligig beetles; fast swimmers on water surfaces in streams.
Haliplidae	Crawling water beetles; small herbivorous beetles in shallow water.
Hydrophilidae	Water scavenger beetles; aquatic or semi-aquatic scavengers.
Latridiidae	Minute brown scavenger beetles; found in decaying plant matter.
Monotomidae	Root-eating beetles; often associated with decaying wood.
Mordellidae	Tumbling flower beetles; found on flowers near riparian habitats.
Nitidulidae	Sap beetles; feed on decaying fruit, fungi, and plant material.
Notonectidae	Backswimmers; aquatic predators that swim upside down.
Panorpidae	Scorpionflies; scavengers, often in damp shaded stream habitats.
Phalacridae	Shining flower beetles; small pollen feeders.
Psylloidea	Psyllids; plant sap-feeders, often on riparian trees and shrubs.
Scirtidae	Marsh beetles; aquatic or semi-aquatic beetles in wetlands.
Staphylinidae	Rove beetles; very diverse predators and scavengers in moist habitats.
Syrphidae	Hoverflies; larvae are aphid predators, adults visit flowers.
Tabanidae	Horse flies; adults feed on blood or nectar, larvae in wet soils.
Vespidae	Wasps; diverse group of predators and parasitoids near water.

Plot data

# Alternative: side-by-side histogram (use 'dodge')
ggplot(d, aes(x = size, fill = location)) +
  geom_histogram(binwidth = 1, color = "black", alpha = 0.7, position = "dodge") +
  labs(
    title = "Histogram of individual sizes by sampled location",
    x = "Size (mm)",
    y = "Frequency",
    fill = "Location"
  ) +
  theme_bw(base_size = 14)

# with stat halfeye
ggplot(d, aes(y = location, x = size, fill = location)) +
  stat_halfeye(position = "dodge",
    adjust = 1,       # smoothness of density
    width = 0.6,        # width of half-eye
    justification = -0.1,
    point_interval = mean_qi,  # show mean & 95% interval
    alpha = 0.7
  ) +
  labs(
    title = "Size Distributions by Location",
    y = "Location",
    x = "Size (mm)"
  ) +
  theme_bw(base_size = 14)

Macrozoobethos

The macrozoobenthos data we are going to use was collected by Ph.D student Valentin Moser , UZH Master student Dominic Tinner and Patrick Hofmann within the WSL-Eawag project: Species interactions in beaver engineered habitats link land-water ecosystem processes. They sampled 14 streams with beaver presence across Switzerland (Figure 3). The streams varied in surrounding landscape (open landscape or forest), beaver pond area, and stream ecomorphology, i.e., the structural stream characteristics.

Figure 3: Map of Switzerland showing the 16 sampled streams in the lowlands. Maps A and B show a more detailed visualisation, focusing on streams in the western (A) and eastern (B) regions of the country. Streams sampled in 2021 are depicted red, in 2022 blue. Sites 15 and 16 were sampled but we lack the individual length estimation. Credits and copyrights to Dominic Tinner.

In each stream, four distinct locations were sampled: the lotic-lentic transition upstream of the dam (inflow), the stagnant water behind the dam (pond), a lotic stream section 25 m downstream of the dam (outflow), and a reach without any influence of beaver engineering (control) Figure 4. The control location was located 500 metres upstream of the main dam at eight sites and 500 metres downstream at the other eight sites. This design assumed that the control location represented the stream habitats as they would have existed prior to the arrival of the beaver in the stream. This assures a comprehensive understanding of the beavers’ effect on the freshwater ecosystem by comparing sections directly affected by the dams (i.e. inflow, pond, outflow) with those in their initial state (control).

Figure 4: Schematic overview of the study design. This illustration depicts the arrangement of sample locations in relation to the beaver dam across the studied streams. Control reaches were set either 500 m upstream of the inflow or 500 m downstream of the outflow, with an equal distributioon of upstream and downstream control reaches across the 16 studied streams. Each sample location was sampled four time consecutively, each focusing on different microhabitats. Additionally, light blue stream colour denotes lotic (fast-flowing) conditions, while dark blue represents the lentic (standing water) conditions in ponds, signifying typical stream current velocity. Credits and copyrights to Dominic Tinner.

The aquatic invertebrate sampling was conducted in May/June of 2021 or 2022 with the kick-net method. During kick-net sampling, the collector kicks up the sediment in a 0.25 x 0.25 meter area of the stream for 20 seconds while a net is placed downstream of the sampling area to collect swirled-up invertebrates. Each sample location (e.g. inflow) was sampled four times consecutively to capture different microhabitats, with two samples in organic substrates (e.g., submerged macrophytes, roots) and two samples in non-organic substrates (e.g., gravel, sand). The content of the net was then transferred to plastic tubs, where aquatic invertebrates were picked out by hand for a duration of Ab minutes. After this time, the remaining content was washed in the stream (similar to gold panning), leaving only fine sediment with remaining individuals. This was stored together with the picked-out invertebrates in [^% ethanol. The sampling in each stream was completed within one day, moving upstream to avoid impacting subsequent samples.

Predictors:

Land use intensity

Land-use intensity data for each study site were extracted by Valentin Moser from Geodienste.ch and swisstopo.admin.ch using ARCGIS (Pro v. 2.8, Esri Inc., 2021 und QGIS 3.40 ‘Bratislava’ 2024). A radius of 250 meters was selected around the centre of each Pool and Control to avoid overlap between paired sampling areas. A visual inspection of the data showed highly reliable classification for agricultural (e.g., crop fields, pastures, areas that farmers maintain for biodiversity) and natural (e.g., forests, riparian areas) land-use. Areas without classified land-use were very often urban areas and human infrastructure, such as streets, railways, and housing. Therefore, missing data was assigned to urban land-use. V. Moser averaged the sum of agricultural, urban, and natural land-use cover types per site across Pool and Control. Agricultural and urban land were summarized into an overall human impact called human_influence.

Stream ecomorphology

The classification of ecomorphology index considered factors such as riparian zone modifications and structural alterations of stream beds to provide an estimate of the degree of anthropogenic impact. The streams included in this study belonged to the first three of the five ecomorphology categories, ranging from near-natural (category level 1) to slightly impacted (2) and heavily impacted (3). The values for ecomorphology were retrieved for each stream from the Swiss Geoportal, specifically the map layer ’Ecomorphology Level F – River reaches‘ (link to access).

Load raw data

m = read_csv(here("data", "raw", "mzb_size_measurements.csv")) |> select(-c(author))

Let’s load the covariates/predictors we are interested in:

# load site info 

site_info <- read_csv(here("data", "raw" , "site_info.csv")) |> select (c(2:5,8,9,19,23)) |> select(-c(site, sample))

Merge data frames:

m1 <- m  |> 
  left_join(site_info, by = "laufnummer") |> 
  select("laufnummer","site","location","taxon","family" ,"taxon_lowest","size","ecomorphology",    "area_pool")

h = read_csv(here("data","raw","landuse_valentin.csv")) |> select(2,7)
# just get the unique value by site 
h_unique <- h  |> 
  distinct(site, human_influence)  |> 
  arrange(site, human_influence)

Merge the human influence variable derived by V. Moser to the macrozoobenthos dataframe:

m2 <- m1  |> 
  left_join(h_unique, by = "site") 

Now we are going to:

• Renames the existing location column to location_old.

• Creates a new column location where the first three categories (inflow, outflow, pool) are all grouped under "beaver", and the fourth category stays as it is.

m3 <- m2 %>%
  rename(location_old = location) %>%            # keep old column
  mutate(location = ifelse(location_old %in% c("Inflow", "Outflow", "Pool"),
                           "beaver",
                           location_old))

Plot the standardized human influence by site:

# standardise human_influence (z-score)
h_std <- h %>%
  mutate(human_influence_std = scale(human_influence)[,1])

# plot
ggplot(h_std, aes(x = site, y = human_influence_std)) +
  geom_point(color = "steelblue", size = 3) +
  theme_minimal() +
  labs(
    title = "Standardised Human Influence by Site",
    x = "Site",
    y = "Human Influence (standardised)"
  ) +
  theme(axis.text.x = element_text(angle = 45, hjust = 1))

The sites with above-average human influence (> 0) are: Biber, Chriesbach, Ellikon, Gaebelbach, Gile, Leugene, Rot, Tegel, Weierbach.

Plot

# Alternative: side-by-side histogram (use 'dodge')
ggplot(m3, aes(x = size, fill = location)) +
  geom_histogram(binwidth = 1, color = "black", alpha = 0.7, position = "dodge") +
  labs(
    title = "Histogram of individual sizes by sampled location",
    x = "Size (mm)",
    y = "Frequency",
    fill = "Location"
  ) +
  theme_bw(base_size = 14)

# Summarize stats per location
stats <- m3 %>%
  group_by(location) %>%
  summarise(
    n = n(),
    mean_size = mean(size, na.rm = TRUE),
    sd_size = sd(size, na.rm = TRUE),
    median_size = median(size, na.rm = TRUE)
  )

# with stat halfeye
ggplot(m3, aes(y = location, x = size, fill = location)) +
  stat_halfeye(
    position = "dodge",
    adjust = 1.1,       
    width = 0.6,        
    justification = -0.1,
    point_interval = mean_qi,  
    alpha = 0.7
  ) +
  geom_text(
    data = stats,
    aes(
      x = 20,                # fixed at 20 mm
      y = location,          # map y to location
      label = paste0("n=", n, "\nmean=", round(mean_size,1),
                     "\nsd=", round(sd_size,1),
                     "\nmedian=", round(median_size,1))
    ),
    inherit.aes = FALSE,
    hjust = 0,
    size = 3.5
  ) +
  labs(
    title = "Size Distributions by Location",
    y = "Location",
    x = "Size (mm)"
  ) +
  theme_bw(base_size = 14)

Terrestrial arthropods

This data was collected by Ph.D student Valentin Moser and Master students in 2021 and 2022 within 16 different streams in Switzerland. They sampled terrestrial arthropods by using a 5 x 1 m plot located one meter from the stream’s edge in the centre of the beaver pool and control area. Within each plot, they sampled the arthropods at the two ends of the 5 x 1 m plot in cylindrical baskets (50 cm diameter, 67 cm height, woven fabric) using suction sampling on a sunny day between 10:00-17:00 during peak arthropod activity. The samples were stored in ethanol, individuals were counted, measured and identified to order level with the help of a binocular.

Load raw data

t21 = readxl::read_xlsx(path = here("data", "raw","data_arthropods_terrestrial_2021.xlsx"), sheet = 1) |> mutate(year = 2021) |> rename(laufnummer = Laufnummer) |> select(-c(remarks,adult))
# load site info 

site_info <- read_csv(here("data", "raw" , "site_info.csv")) |> select (c(2:5,8,9,19,23)) 
# check common columns 
intersect(names(t21), names(site_info))

[1] "laufnummer"

# meerge site info to t21 df 
t21_merged <- t21 %>%
  left_join(site_info, by = "laufnummer") |> 
  select(latitude_sample, longitude_sample,laufnummer, year, site, sample,location, ecomorphology, area_pool, everything())

# To see rows with NA in size
t21_merged %>% filter(is.na(size))

# A tibble: 1 × 15
  latitude_sample longitude_sample laufnummer  year site  sample    location
            <dbl>            <dbl>      <dbl> <dbl> <chr> <chr>     <chr>   
1            47.6             9.18         72  2021 Logge Outflow_3 Outflow 
# ℹ 8 more variables: ecomorphology <dbl>, area_pool <dbl>,
#   samples_replicate <chr>, class <chr>, order <chr>, suborder <chr>,
#   family <chr>, size <dbl>

Remove NAs

References